| ... | ... | @@ -16,7 +16,6 @@ I added a new script in `/bioinf/transfer/marmic_NGS2022/software` called `FastA |
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For the assembly of the metagenomic samples we are going to use megahit. Be sure to also check out other assemblers such as IDBA-ud and SPAdes.
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First, make sure it is available. It should be included in the marmic2022 conda environment.
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| ... | ... | @@ -38,15 +37,15 @@ $ megahit -m 0.2 -1 G.1.fa -2 G.2.fa -o G-{your-assigned-kmer} -t 8 --min-contig |
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| Student | k-mer | `#` contigs (>500bp) | N50 and L50 | Longest contig (bp) | Total length (bp) |
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|---------|-------|----------------------|-------------|---------------------|-------------------|
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| | 33 | | | | |
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| Leonard | 33 | | | | |
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| | 37 | | | | |
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| | 43 | | | | |
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| | 47 | | | | |
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| | 53 | | | | |
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| | 57 | | | | |
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| | 63 | | | | |
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| | 67 | | | | |
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| | 73 | | | | |
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| Louison | 43 | | | | |
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| Ava | 47 | | | | |
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| Ella | 53 | | | | |
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| Kinga | 57 | | | | |
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| Nicole | 63 | | | | |
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| Margret | 67 | | | | |
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| Mahum | 73 | | | | |
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The assembly of samples using single k-mer sizes should take <span dir="">\~</span> 10 minutes. Once you have an assembly, you can use the stats.sh program from bbmap (/bioinf/software/bbmap) on the contigs file to get some basic information about it.
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